chr16-2830720-T-C

Variant names:

• chr16-2830720-T-C
• rs868622753
• NM_145252.3:c.79T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_145252.3(ZG16B):​c.79T>C​(p.Tyr27His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: ZG16B NM_145252.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.578
• Publications: 0 publications found

Genes affected

ZG16B (HGNC:30456): (zymogen granule protein 16B) Predicted to enable carbohydrate binding activity. Involved in retina homeostasis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08406025).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145252.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZG16B	NM_145252.3	MANE Select	c.79T>C	p.Tyr27His	missense	Exon 3 of 4	NP_660295.3	Q96DA0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZG16B	ENST00000382280.8	TSL:1 MANE Select	c.79T>C	p.Tyr27His	missense	Exon 3 of 4	ENSP00000371715.4	Q96DA0
	ZG16B	ENST00000572863.2	TSL:2	c.79T>C	p.Tyr27His	missense	Exon 2 of 3	ENSP00000461740.2	Q96DA0
	ZG16B	ENST00000902257.1		c.79T>C	p.Tyr27His	missense	Exon 3 of 4	ENSP00000572316.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.65
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.5
DANN	Benign	0.66
DEOGEN2	Benign	0.019	T
Eigen	Benign	-1.0
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.012	N
M_CAP	Benign	0.0032	T
MetaRNN	Benign	0.084	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.2	L
PhyloP100		-0.58
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.018
Sift	Benign	0.18	T
Sift4G	Uncertain	0.0040	D
Polyphen		0.41	B
Vest4		0.18
MutPred		0.37		Loss of sheet (P = 0.0025)
MVP		0.014
MPC		0.062
ClinPred		0.18	T
GERP RS		-1.5
PromoterAI		0.0063	Neutral
Varity_R		0.20
gMVP		0.16

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs868622753; hg19: chr16-2880721;